myokit 1.33.9__py3-none-any.whl → 1.35.0__py3-none-any.whl

myokit/formats/cuda/__init__.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from ._exporter import CudaKernelExporter, CudaKernelRLExporter
 from ._ewriter import CudaExpressionWriter
 from myokit.formats import ansic

myokit/formats/cuda/_ewriter.py

@@ -4,10 +4,8 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import myokit
+
 from myokit.formats.python import PythonExpressionWriter
 
 
@@ -17,7 +15,7 @@ class CudaExpressionWriter(PythonExpressionWriter):
     Myokit :class:`expressions <myokit.Expression>` to their CUDA equivalents.
     """
     def __init__(self, precision=myokit.SINGLE_PRECISION):
-        super(CudaExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = ''
         self._sp = (precision == myokit.SINGLE_PRECISION)
 

myokit/formats/cuda/_exporter.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import os
 
 import myokit.formats

myokit/formats/cuda/template/kernel.cu

@@ -66,13 +66,16 @@ model.reserve_unique_names(
     )
 model.create_unique_names()
 
+# Get initial values (before time binding is removed and model becomes invalid)
+initial_values = model.initial_values(True)
+
 # Process bindings, remove unsupported bindings, get map of bound variables to
 # internal names
-bound_variables = model.prepare_bindings({
+bound_variables = myokit._prepare_bindings(model, {
     #'time' : 'time',
     #'pace' : 'pace',
     'diffusion_current' : 'I_diff',
-    })
+})
 
 # Get equations
 equations = model.solvable_order()
@@ -190,7 +193,7 @@ for group in equations.values():
 print('')
 print('/* Aliases of state variables. */')
 for var in model.states():
-    print('#define ' + var.uname() + ' state[' + str(var.indice()) + ']')
+    print('#define ' + var.uname() + ' state[' + str(var.index()) + ']')
 
 ?>
 
@@ -295,10 +298,10 @@ int get_default_initial_state(Real *state)
     if (state == 0) return(-1);
 
 <?
-for var in model.states():
+for var, val in zip(model.states(), initial_values):
     if 'desc' in var.meta:
         print(tab + '// ' + var.meta['desc'])
-    print(tab + v(var) + ' = ' + myokit.float.str(var.state_value()) + ';')
+    print(tab + v(var) + ' = ' + myokit.float.str(val) + ';')
 ?>
 
     return(0);

myokit/formats/easyml/__init__.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from ._exporter import EasyMLExporter
 from ._ewriter import EasyMLExpressionWriter
 

myokit/formats/easyml/_ewriter.py

@@ -4,12 +4,10 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import warnings
 
 import myokit
+
 from myokit.formats.python import PythonExpressionWriter
 
 
@@ -19,7 +17,7 @@ class EasyMLExpressionWriter(PythonExpressionWriter):
     equations for variables in EasyML syntax.
     """
     def __init__(self):
-        super(EasyMLExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = ''
 
     #def _ex_name(self, e):
@@ -39,7 +37,7 @@ class EasyMLExpressionWriter(PythonExpressionWriter):
         if isinstance(e[1], myokit.Exp) and isinstance(e[0], myokit.Number):
             if e[0].eval() == 1:
                 return '-expm1(' + self.ex(e[1][0]) + ')'
-        return super(EasyMLExpressionWriter, self)._ex_minus(e)
+        return super()._ex_minus(e)
 
     #def _ex_multiply(self, e):
     #def _ex_divide(self, e):
@@ -58,23 +56,23 @@ class EasyMLExpressionWriter(PythonExpressionWriter):
 
     def _ex_sin(self, e):
         warnings.warn('Potentially unsupported function: sin()')
-        return super(EasyMLExpressionWriter, self)._ex_sin(e)
+        return super()._ex_sin(e)
 
     #def _ex_cos(self, e):
 
     def _ex_tan(self, e):
         warnings.warn('Potentially unsupported function: tan()')
-        return super(EasyMLExpressionWriter, self)._ex_tan(e)
+        return super()._ex_tan(e)
 
     def _ex_asin(self, e):
         warnings.warn('Potentially unsupported function: asin()')
-        return super(EasyMLExpressionWriter, self)._ex_asin(e)
+        return super()._ex_asin(e)
 
     #def _ex_acos(self, e):
 
     def _ex_atan(self, e):
         warnings.warn('Potentially unsupported function: atan()')
-        return super(EasyMLExpressionWriter, self)._ex_atan(e)
+        return super()._ex_atan(e)
 
     #def _ex_exp(self, e):
 
@@ -87,11 +85,11 @@ class EasyMLExpressionWriter(PythonExpressionWriter):
 
     def _ex_floor(self, e):
         warnings.warn('Potentially unsupported function: floor()')
-        return super(EasyMLExpressionWriter, self)._ex_floor(e)
+        return super()._ex_floor(e)
 
     def _ex_ceil(self, e):
         warnings.warn('Potentially unsupported function: ceil()')
-        return super(EasyMLExpressionWriter, self)._ex_ceil(e)
+        return super()._ex_ceil(e)
 
     def _ex_abs(self, e):
         return self._ex_function(e, 'fabs')

myokit/formats/easyml/_exporter.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import collections
 import os
 import warnings
@@ -372,8 +369,8 @@ class EasyMLExporter(myokit.formats.Exporter):
 
             # Write initial conditions
             for v in model.states():
-                f.write(lhs(v) + '_init = ' + myokit.float.str(v.state_value())
-                        + eos)
+                f.write(lhs(v) + '_init = '
+                        + myokit.float.str(v.initial_value(True)) + eos)
             f.write(eol)
 
             # Write remaining variables

myokit/formats/html/__init__.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from ._exporter import HTMLExporter
 from ._flatten import html2ascii    # noqa
 

myokit/formats/html/_exporter.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from lxml import etree
 
 import myokit

myokit/formats/html/_flatten.py

@@ -4,19 +4,11 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
+import html
+import html.parser
 import re
-import sys
 import textwrap
 
-# HTML Parser in Python 2 and 3
-try:
-    from HTMLParser import HTMLParser
-except ImportError:
-    from html.parser import HTMLParser
-
 
 def html2ascii(html, width=79, indent='  '):
     """
@@ -32,21 +24,13 @@ def html2ascii(html, width=79, indent='  '):
     return f.get_text()
 
 
-class Asciifier(HTMLParser):
+class Asciifier(html.parser.HTMLParser):
     INDENT = 1
     DEDENT = -1
     WHITE = [' ', '\t', '\f', '\r', '\n']
 
     def __init__(self, line_width=79, indent='  '):
-        if sys.hexversion < 0x03000000:     # pragma: no python 3 cover
-            # HTMLParser requires old-school constructor
-            HTMLParser.__init__(self)
-        else:                               # pragma: no python 2 cover
-            super(Asciifier, self).__init__(convert_charrefs=False)
-
-            # Unescape method is deprecated
-            import html
-            self.unescape = html.unescape
+        super().__init__(convert_charrefs=False)
 
         # In <head> yes/no
         self.inhead = False
@@ -226,7 +210,7 @@ class Asciifier(HTMLParser):
             return
 
         # Convert html characters
-        data = self.unescape('&' + name + ';')
+        data = html.unescape('&' + name + ';')
 
         # Convert to ascii and back to strip out non-ascii content
         data = data.encode('ascii', 'ignore').decode('ascii')

myokit/formats/latex/__init__.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from ._exporter import PdfExporter, PosterExporter
 from ._ewriter import LatexExpressionWriter
 

myokit/formats/latex/_ewriter.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import myokit.formats
 
 
@@ -16,7 +13,7 @@ class LatexExpressionWriter(myokit.formats.ExpressionWriter):
     Myokit :class:`expressions <myokit.Expression>` to their Tex equivalent.
     """
     def __init__(self):
-        super(LatexExpressionWriter, self).__init__()
+        super().__init__()
 
         # Default time variable
         self._time = None

myokit/formats/latex/_exporter.py

@@ -4,12 +4,10 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import os
 
 import myokit
+
 from ._ewriter import LatexExpressionWriter
 
 
@@ -19,7 +17,7 @@ class PdfExporter(myokit.formats.Exporter):
     a simple latex document.
     """
     def __init__(self):
-        super(PdfExporter, self).__init__()
+        super().__init__()
 
     def _clean(self, text):
         """
@@ -76,7 +74,7 @@ class PdfExporter(myokit.formats.Exporter):
                 f.write('\\begin{dmath}\n')
                 f.write(e.ex(myokit.Name(v)))
                 f.write(' = ')
-                f.write(e.ex(myokit.Number(v.state_value())))
+                f.write(e.ex(v.initial_value()))
                 f.write('\\end{dmath}\n')
 
             # Write each component
@@ -111,7 +109,7 @@ class PosterExporter(myokit.formats.Exporter):
     beholders.
     """
     def __init__(self):
-        super(PosterExporter, self).__init__()
+        super().__init__()
 
     def post_export_info(self):
         return '\n'.join((

myokit/formats/mathml/__init__.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from ._ewriter import MathMLExpressionWriter
 from ._parser import (   # noqa
     MathMLError,

myokit/formats/mathml/_ewriter.py

@@ -4,19 +4,10 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from lxml import etree
 
 import myokit.formats
 
-# Strings in Python 2 and 3
-try:
-    basestring
-except NameError:   # pragma: no cover
-    basestring = str
-
 
 class MathMLExpressionWriter(myokit.formats.ExpressionWriter):
     """
@@ -25,7 +16,7 @@ class MathMLExpressionWriter(myokit.formats.ExpressionWriter):
     Presentation MathML.
     """
     def __init__(self):
-        super(MathMLExpressionWriter, self).__init__()
+        super().__init__()
 
         # Default mode
         self._pres = False
@@ -33,7 +24,7 @@ class MathMLExpressionWriter(myokit.formats.ExpressionWriter):
         # Default lhs conversion function
         def flhs(lhs):
             var = lhs.var()
-            if isinstance(var, basestring):
+            if isinstance(var, str):
                 # This can happen with time variable of derivative if the
                 # proper variable isn't set!
                 return var

myokit/formats/mathml/_parser.py

@@ -4,10 +4,8 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import myokit
+
 from myokit.formats.xml import split
 
 
@@ -63,10 +61,10 @@ class MathMLError(myokit.ImportError):
                 message = 'Error on line ' + line + '. ' + message
             except AttributeError:
                 pass
-        super(MathMLError, self).__init__(message)
+        super().__init__(message)
 
 
-class MathMLParser(object):
+class MathMLParser:
     """
     Parses MathML expressions into :class:`myokit.Expression` objects.
 
@@ -84,7 +82,7 @@ class MathMLParser(object):
         will be added to this set.
 
     This is not a validating parser: if the MathML is invalid the method's
-    behaviour is undefined.
+    behavior is undefined.
 
     The following MathML elements are recognised:
 

myokit/formats/matlab/__init__.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from ._exporter import MatlabExporter
 from ._ewriter import MatlabExpressionWriter
 

myokit/formats/matlab/_ewriter.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from myokit.formats.python import PythonExpressionWriter
 
 
@@ -16,7 +13,7 @@ class MatlabExpressionWriter(PythonExpressionWriter):
     Myokit :class:`expressions <myokit.Expression>` to a Matlab syntax.
     """
     def __init__(self):
-        super(MatlabExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = ''
         self._fcond = 'ifthenelse'
 

myokit/formats/matlab/_exporter.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import os
 
 import myokit.formats
@@ -67,7 +64,7 @@ class MatlabExporter(myokit.formats.TemplatedRunnableExporter):
         # Variable naming function
         def v(var):
             if isinstance(var, myokit.Derivative):
-                return 'ydot(' + str(1 + var.var().indice()) + ')'
+                return 'ydot(' + str(1 + var.var().index()) + ')'
             if isinstance(var, myokit.Name):
                 var = var.var()
             if var.is_constant():
@@ -81,7 +78,7 @@ class MatlabExporter(myokit.formats.TemplatedRunnableExporter):
         ew.set_condition_function('ifthenelse')
 
         # Process bound variables
-        bound_variables = model.prepare_bindings({
+        bound_variables = myokit._prepare_bindings(model, {
             'time': 't',
             'pace': 'pace',
         })

myokit/formats/matlab/template/main.m

@@ -5,6 +5,7 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
+import myokit
 ?>%
 % Driver file for <?= model.name() ?>
 %
@@ -15,8 +16,8 @@ clear all
 
 % Initial values
 <?
-for eq in model.inits():
-    print(e(eq) + ';')
+for var, value in zip(model.states(), model.initial_values(True)):
+    print(v(var) + ' = ' + myokit.float.str(value) + ';')
 ?>
 
 % Vector for initial values

myokit/formats/opencl/__init__.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 from ._exporter import OpenCLExporter, OpenCLRLExporter
 from ._ewriter import OpenCLExpressionWriter
 from myokit.formats import ansic

myokit/formats/opencl/_ewriter.py

@@ -4,10 +4,8 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import myokit
+
 from myokit.formats.python import PythonExpressionWriter
 
 
@@ -17,7 +15,7 @@ class OpenCLExpressionWriter(PythonExpressionWriter):
     Myokit :class:`expressions <myokit.Expression>` to OpenCL syntax.
     """
     def __init__(self, precision=myokit.SINGLE_PRECISION, native_math=True):
-        super(OpenCLExpressionWriter, self).__init__()
+        super().__init__()
         self._function_prefix = ''
         self._sp = (precision == myokit.SINGLE_PRECISION)
         self._nm = bool(native_math)

myokit/formats/opencl/_exporter.py

@@ -4,9 +4,6 @@
 # This file is part of Myokit.
 # See http://myokit.org for copyright, sharing, and licensing details.
 #
-from __future__ import absolute_import, division
-from __future__ import print_function, unicode_literals
-
 import os
 
 import myokit.formats
@@ -44,7 +41,7 @@ class OpenCLExporter(myokit.formats.TemplatedRunnableExporter):
             'kernel.cl': 'kernel.cl',
             'plot.py': 'plot.py',
             'minilog.py': 'minilog.py',
-            'test': 'test',
+            'test.sh': 'test.sh',
         }
 
     def _vars(self, model, protocol):
@@ -80,7 +77,7 @@ class OpenCLExporter(myokit.formats.TemplatedRunnableExporter):
 
         # Process bindings, remove unsupported bindings, get map of bound
         # variables to internal names.
-        bound_variables = model.prepare_bindings({
+        bound_variables = myokit._prepare_bindings(model, {
             'time': 'time',
             'pace': 'pace',
             'diffusion_current': 'idiff',

myokit/formats/opencl/template/cable.c

@@ -192,7 +192,7 @@ void set_initial_values(int n_cells, Real* s)
     for(i=0; i<n_cells; i++) {
 <?
 for v in model.states():
-    print(tab*2 + '*s = ' + myokit.float.str(v.state_value()) + '; s++; // ' + str(v.qname()))
+    print(tab*2 + '*s = ' + myokit.float.str(v.initial_value(True)) + '; s++; // ' + str(v.qname()))
 ?>
     }
 }
@@ -234,14 +234,14 @@ int run(const int n_cells, const Real time_start, const Real time_end, const Rea
     cl_device_id device_id = get_device_id();
     char buffer[65536];
     ocl(clGetDeviceInfo(device_id, CL_DEVICE_NAME, sizeof(buffer), buffer, NULL));
-    printf("Using device: %s\n", buffer);
+    // printf("Using device: %s\n", buffer);
 
     /* Create a context and command queue */
     cl_int err;
     context = clCreateContext(NULL, 1, &device_id, NULL, NULL, &err);
     ocl_check("clCreateContext", err);
     command_queue = clCreateCommandQueue(context, device_id, 0, &err);
-    printf("Created context and command queue.\n");
+    // printf("Created context and command queue.\n");
 
     /* Create state vector */
     int dsize_state = n_cells * n_state * sizeof(Real);
@@ -258,12 +258,12 @@ int run(const int n_cells, const Real time_start, const Real time_end, const Rea
     ocl_check("clCreateBuffer mbuf_state", err);
     mbuf_idiff = clCreateBuffer(context, CL_MEM_READ_ONLY, dsize_idiff, NULL, &err);
     ocl_check("clCreateBuffer mbuf_idiff", err);
-    printf("Created buffers.\n");
+    // printf("Created buffers.\n");
 
     /* Copy data into buffers */
     ocl(clEnqueueWriteBuffer(command_queue, mbuf_state, CL_TRUE, 0, dsize_state, state, 0, NULL, NULL));
     ocl(clEnqueueWriteBuffer(command_queue, mbuf_idiff, CL_TRUE, 0, dsize_idiff, idiff, 0, NULL, NULL));
-    printf("Set initial state.\n");
+    // printf("Set initial state.\n");
 
     /* Load and compile the kernel program(s) */
     char* source = read_kernel("kernel.cl");
@@ -285,14 +285,14 @@ int run(const int n_cells, const Real time_start, const Real time_end, const Rea
         abort();
     }
     ocl_check("clBuildProgram", err);
-    printf("Program created and built.\n");
+    // printf("Program created and built.\n");
 
     /* Create the kernels */
     kernel_cell = clCreateKernel(program, "cell_step", &err);
     ocl_check("clCreateKernel", err);
     kernel_diff = clCreateKernel(program, "diff_step", &err);
     ocl_check("clCreateKernel", err);
-    printf("Kernels created.\n");
+    // printf("Kernels created.\n");
 
     /* Pass arguments into kernels */
     ocl(clSetKernelArg(kernel_cell, 0, sizeof(n_cells), &n_cells));
@@ -304,7 +304,7 @@ int run(const int n_cells, const Real time_start, const Real time_end, const Rea
     ocl(clSetKernelArg(kernel_diff, 1, sizeof(g), &g));
     ocl(clSetKernelArg(kernel_diff, 2, sizeof(mbuf_state), &mbuf_state));
     ocl(clSetKernelArg(kernel_diff, 3, sizeof(mbuf_idiff), &mbuf_idiff));
-    printf("Arguments passed into kernels.\n");
+    // printf("Arguments passed into kernels.\n");
 
     /* Add log header */
     printf("engine.time");
@@ -342,7 +342,7 @@ for v in model.states():
 
 done:
     /* Tidy up */
-    printf("Tidying up.\n");
+    // printf("Tidying up.\n");
 
     ocl(clFlush(command_queue));
     ocl(clFinish(command_queue));
@@ -356,7 +356,7 @@ done:
     free(state);
     free(idiff);
 
-    printf("Done.\n");
+    // printf("Done.\n");
 }
 
 int main()

myokit/formats/opencl/template/kernel.cl

@@ -140,7 +140,7 @@ for group in equations.values():
 print('')
 print('/* Aliases of state variables. */')
 for var in model.states():
-    print('#define ' + var.uname() + ' state[offset + ' + str(var.indice()) + ']')
+    print('#define ' + var.uname() + ' state[offset + ' + str(var.index()) + ']')
 
 print('')
 for comp, ilist in comp_in.items():

myokit/formats/opencl/template/minilog.py

@@ -69,7 +69,7 @@ class DataLog(OrderedDict):
         # Delimiters
         quote = '"'
         delim = ','
-        with open(filename, 'rb') as f:
+        with open(filename, 'r', newline=None) as f:
             # Read header
             keys = []
             try: